Naruto - evolution
by Kingdark
Summary: Naruto is taken by future apocalypse to prevent his own defeat. He takes Naruto before he has a chance to mature into the warrior he fears of the future. F-apocalypse changes Naruto so he would be one of the most powerful warriors of the planet and utterly, completely loyal to him. Fortunately, or unfortunately, Naruto is only found shortly before the brain washing could begin...
1. Chapter 1

Naruto: evolution

Short summary: Naruto is taken by future apocalypse to prevent his own defeat. He takes Naruto before he has a chance to mature into the warrior he fears of the future. F-apocalypse changes Naruto so he would be one of the most powerful warriors of the planet and utterly, completely loyal to him. Fortunately, or unfortunately, Naruto is only found shortly before the brain washing could begin...

Complete summary: Naruto is taken after the forbidden scrolls fiasco by the Apocalypse, who came back in the past after being defeated in the future. Future Apocalypse meant his past self to find Naruto in order to prevent his own defeat. Using all the impressive technologies that future-Apocalypse has at his disposal, he modifies Naruto's genes to have the powers of some of the most powerful mutant of his time. Thankfully his plans are all for naught when Naruto is found just before the brainwashing could begin...

**I got this idea from reading a story that already exists. I used a lot as a guideline. The next chapter will be entirely different or at least different enough that I can't be accused of stealing. If you recognize parts of the writing then that's because I left it as it was. This entire chapter is not identical though. That's just not nice. Just some parts are.**

**This happens during 'x-men first generation'**

**Kingdark**

Naruto: evolution

Chapter 01

Two men moved silently down a darkened tunnel that hadn't been entered for months. Dust and other dirt had begun to pile up but not enough that it would be really noticeable. Both men were obvious experienced fighters but also seemed to carry an invisible weight. Something that weighted them down. Right now they were moving with a firm goal in mind and these two had grown very close friends. Best friends even.

Both men were around the same age but couldn't look any more different. The first of the two was dressed in black slacks and a green jacket. The other dressed in a suit of red body armour. He wore a pair of black gloves and knee high boots.

"Are you sure this is the place, Charles?"

"Of course I am Erik. This is definitely the place, Cerebro is never wrong."

That was an understatement of course. Cerebro was a piece of technology that was very advanced compared to the technology available to the common man. It allowed Charles to use it as a focus with its sole purpose finding mutants. It could detect normal humans as well but it was primarily designed to find and locate mutants. Especially the stronger ones. The idea behind the creation of Cerebro was not just to find mutants but also to teach them and to help them control their powers.

Erik knew that Charles was right of course. After all, he had helped him built Cerebro in the first place and knew how it worked. It gave Charles not only the location of a mutant but also told Charles how strong said mutant was. Only the two of them and one other knew the details how to make another. The two men continued walking down the tunnel.

After ten minutes of dropping deeper under the surface they exited the tunnel into an underground base. It was completely abandoned, proven by the fact that only emergency lights were active and that there was no response to their intrusion. Then there was the fact that Charles couldn't sense anyone except the two of them and as far as the two of them knew, there was nothing that could black Charles telepathy.

Charles held up his hand to make Erik stop for a few moments. "There are a few cleverly hidden traps ready to be triggered by pressure plates. Follow me exactly. I don't want the security system to go off. Something tells me that the technology here is far more advanced then anything available on the planet. Or a hundred years from now."

Erik said nothing. The statement caught him off guard but he went on high alert still. Charles 'guess' was an understatement if anything. The weapons available in some of the rooms, not to mention the technology hinted at something extraordinary.

"I have a feeling I won't like what we'll find." Erik muttered.

"So do I." Charles agreed.

"Tell me why we had to do this in secret again?"

"Because this mutant is possibly the most powerful mutant I've ever sensed. We both know what the government might do if they discover a mutant with the possible power that this one has..."

Erik snorted. Of course they knew. It was only because of Charles telepathy and his uncanny ability for finding blackmail that they weren't test subjects in some random lab.

"We've arrived." Said Charles suddenly.

The two of them stopped before a door of solid steel. Erik tested the metal at it barely reacted at all. "This isn't normal steel Charles." Erik said cautiously. "It barely reacts to my commands at all."

"Let me give it a try. Maybe there is some computer equipment that I can use to open..." Charles trailed off as he automatically closed his eyes in to concentrate.

A few moments later they heard dozens of locks and other security measures disengage. "It was a good thing you didn't force it." Charles said after a moment. "It would have activated every defence in the base AND the self destruct system. If I'm right it would have enough explosives to... Well it would be a very strong explosion." Charles finished. "I'm not sure I can give a fair guess as to how powerful it would be."

"Let's move onwards instead." Erik said after a moment.

"Right." Charles agreed. "We can check the computer for details later. Erik..."

"Yes?"

"If this base is truly as advanced as it seems..."

"I know." Erik said after a moment.

The two of them stared at each other. Erikwas comfortable enough with his friend to exchange thoughts and idea's as they popped up. You would be surprised how quickly you can come to a solution if you can communicate like that."

"Let's wait until later then." Charles acknowledged.

It was only now that both noticed a seat of initials that were repeated throughout the lab. Like a national flag or something. "I wonder what A-O means." Erik muttered lowly.

As soon as both of them entered the room, lights activated on their own as did various computer screens. More importantly it light up the machine in the middle of the lab. The sight that greeted them was something they had... Expected but not wanted to see. They hadn't wanted to think on the details. Hadn't wanted to accept the reality of the matter. In the middle of the room wasa machine that held a glass tube. Within said tube was a boy around his teenager years. The teenager was completely nude with only the required tubes to remove body waste.

Erik could sense the anger of his friend and he couldn't blame him. Charles always tried to see the world as positively as he could. Not wanting to acknowledge the darker parts of humanity. Perhaps now he would agree when they had their next debate.

"My god what have they done to him?" asked Charles in shock. "The same what they did to Logan I'm sure. Or similar to at least." Erik said darkly.

Charles had moved towards the computer terminal and logged in with the details on hand. "If there was a single doubt that this equipment was of the future... Then there is no doubt now." Charles said after a moment. It took him a few moments to get used to the system but eventually he managed to summon the information he wanted.

Suddenly a transparent figure emerged in the centre of the room.

The figure was a giant standing at least seven foot tall and was very muscular. His skin was grey and eyes were red. He wore a pair of deep blue shorts along with a muscle shirt of the same colour with a pair of gloves and boots.

"If you are seeing this then you have finally awakened and found this little base. As you can probably guess I'm you. Only I'm you from the future. Or a future. That sort of thing gives me... Us always a headache. In the future I take up the name of apocalypse and in the future I have been defeated by the very child I have taken here in this chamber. The child in the tube is Namikaze Naruto except he only knows himself as Uzumaki Naruto. When I first encountered him, we fought and I lost badly. I lost because I underestimated him and I lived to tell about it because of his kind nature." The figure paused and began to pace.

"The only reason I can tell you this now is because I'm spending all my energy to keep myself together. Once this is done I'll die and nothing will remain of me. I came back from the future to prevent my own defeat and what else is a better solution then to make a trusted ally of the one that defeated me? By the time he is twenty four, the age where we first met he is a greater warrior, and more powerful then Charles Xavier from his band of heroes he called the x-men and Magneto's brotherhood of mutants."

Charles and Erik both startled when they were referred to. Not together but what it implied... "Does this mean we'll become enemies in the future?" Charles wondered. Erik didn't respond because he knew that it wasn't that ridiculous.

"Naruto... Naruto was the leader of his village. A village full of mutants that somehow had a long history of their own. A whole continent that existed in another dimension at the same time it did as our own world and Naruto... That same boy was the sole survivor of his entire people. He proved time and time again why he had been acknowledged as a double S class ninja. I'm not going to waste time by going into detail because I recorded all of it in the computer here should you be interested."

"This is Naruto when he is an adult." Future-Apocalypse was replaced with the same child only he was much older. He stood roughly six feet in height, wore black pants that were taped down with white bandages. He wore a dark orange vest that had signs of being custom made because of the black flames printed on them. Finally, the older Naruto wore a forehead protector that had a spiral edged into it with a small arrow attached to it. The plate was held in place by a long strip of black cloth and was tied to his forehead.

"This man was capable of summoning toads, dogs, birds, salamanders... And all of them were the size of three story houses." Each example was replaced by a picture.

"Naruto is capable of regeneration, super strength, reflexes that no regular human can repeat and a strong sense of smell and taste. All of these attributes don't even make Naruto unusual among his people. Naruto could manipulate fire, wind, earth and just about any other combination he wished and all of these things are still connected to the energy all of his people can manipulate."

"Naruto's people discovered that there is a way to control their mutation. To control it from a young age. Their unusual mutations are gathered in clans and are highly valued. They were encouraged to breed with the hopes of creating more children with the same power. Chakra, they call it my younger self. Know how to manipulate chakra and you can unite all mutants under one banner. These people have developed hundreds if not thousands different techniques... This makes them highly valuable."

"And do you know what the funniest thing is of all? His potential is suppressed! On the continent where this child lived, there were nine powerful creatures. Nine beasts of pure energy. Of negative energy. At some point they were captured and sealed in human infants. Eventually they were used as weapons but a few things remained the same. These children that carried these beasts were feared and loathed. They were treated as garbage and this same boy is no different. The beast he carries though is actively suppressing his potential until the boy manages to conquer the beast for himself. It is only then that they get respect for the other and the child is no longer restrained in what he can become and STILL it isn't his mutation."

"This guy sure likes to talk doesn't he?" Charles muttered.

Erik snorted but didn't say anything.

"I took the boy after he was tricked. He was tricked in stealing a highly valued scroll. I took him away before anyone could find him. I took him just so he could find that he is a wanted criminal to be killed on sight." The figure shrugged. "You can tell the child what you wish, but if I were you I would tell it so he would begin to hate it. That he would want to destroy the village and take its shinobi as slaves. It would be the ultimate irony considering he always wanted to be Hokage. The strongest of the village and ultimate protector of it..."

The figure shook his head and glared at the tube. "They say no plan survives the plan with the enemy and I would say they are right. The beast that Naruto held must have sensed me because it attacked the seal and let itself be absorbed. It no longer restrains the child in any form. It has given the child a form of healing that could probably regrow a hand, arm or even a leg. I did tests and only wolverine of the x-men can match Naruto's ability to heal.

"And now I come to my best plan I ever thought of. A plan that will either spell our defeat... Or our guarantee of victory.

"I have stolen the DNA of several powerful mutants of my time and this one. But I'm not as foolish to just dump it into his system and hope for the best. Even though I will die should I ever lose concentration that doesn't mean anything. I used my technology to put this base in a localized bubble of time. I visited the future and stole technology as was needed. Trust me when I say that the boy will mature and have the mutations of the ones I stole as if he were born with them. The power of Charles Xavier, the power of his enemy and ally alike, Magneto and many others. If you can get his loyalty he'll do what you want no matter what. But if you betray him... If there is one negative point it is the fact that there is no way to control him. No way to limit his power. Help him control them yes but not seal it away."

"The bonding of the adamantium should be complete by the time you find him, so he'll be like wolverine in this. Be careful and vigilant with the mental conditioning my younger self. Don't go overboard with it because he has a brilliant mind. The best way is to make him loyal on his own. But If I know myself as well as I do... Do as you wish." The hologram faded after that.

"Charles.." Erik muttered.

Charles looked at his friend. His own emotions were clear to see. This child had enough raw power to be a world wide threat should he ever go bad. But did they had the right to kill him before it ever became an issue?

"We can teach him values Erik..." Charles muttered. He looked his friend straight in the eye. "I know your opinion over certain things but even you should know that if Naruto ever goes bad... Truly bad... That the damage he could do would be enormous. There would be virtually nothing to stop him."

"I know." Erik acknowledged.

"He has no reason to trust us though..." Erik pointed out.

"We could tell him the truth." Charles ventured.

"And then what?" Erik challenged.

"There is a lot in here to be angry about. A lot of secrets kept from him. Hell, anyone would be right to be angry. To be hated because of something you were born with."

"We wake him up." Charles decided. "He'll have my power so he'll know we mean well. We can teach him and then he can return to his village. Where is that scroll that apocalypse mentioned?"

"Over there." Erik gestured.

The scroll was in decent shape so they would keep it safe in a high security safe.

Charles accessed the computer again. "The conditioning hasn't started yet. Apparently, his younger self was supposed to make the decision."

'Get rid of it." Erik ordered.

Charles nodded his agreement. After he made the decision, the tube light up once more.

FINAL STAGE ACTIVATED. SEALS BEING IMPRINTED NOW.

Both men blinked several times. "What does that mean?" Erik wondered.

Charles finger's flew over the keyboard as he hurried to find an answer. "It's a safety measure. A way to control his powers and to activate them when he is ready for them." Charles read from his screen.

"Catch him Erik" Charles barked when he noted the tube was draining and his friend was lost in thought.

Erik snapped out of it and was just in time to catch the teenager in his arms.

"I'm going to put all the data on the servers on these disks. I'll arrange that the hardware will be transported to my home before this whole base will self destruct."

Thirty disks later and it was complete. It was an enormous amount of data and when they explored the base they realized it was FAR bigger then they had thought. This required more manpower then they had available...

X

Weeks later...

Sarutobi Hiruzen frowned as he looked upon the faces of his two loyal students, Jiraiya and Tsunade. He had called for them for the first time in years and had just told them of the disappearance of their godson. Or rather why they found out that their godson was a wanted criminal. At twelve years old! The look he received from them would've been enough to kill anyone else. This was mostly because he had lied and told them originally the boy had died the night he was born. Suddenly the doors opened and two people entered the room getting raised eyebrows from the group of three.

Their meeting was interrupted when the door of his office opened and two men were allowed in. Hiruzen frowned when his ANBU allowed these foreigners inside when he had told them that there were to be no interruptions.

"I wouldn't blame your bodyguards Hokage-san." The bald men said rather rudely.

"There are pieces of information I have in my possession I think you'll all find very interesting. Where your godson is and just why he was declared a criminal. Why you thought him dead perhaps..." Charles gave them a look. "I haven't kidnapped him. In fact, if anything I would be a rescuer. I told Naruto everything I know, and he knows that I haven't lied to him because it's pretty much impossible to lie to him now." Charles said. He used these words to confuse them and to make them ask the obvious question.

"What do you mean, he can't be lied to?" Hiruzen demanded.

"I am a mutant, Hokage-san which means I have something in my body giving me an ability. It is what you know as a bloodline limit. My ability allows me to hear the thoughts of anyone I wish and send my own thoughts to anyone I wish. Nobody can lie to me because it's only a matter of checking your memories to confirm them."

"Are you telling me that Naruto has such an ability? That's impossible! His father didn't have something like that and neither did his mother!" Jiraiya argued.

Charles shrugged. "I haven't finished have I?" And so Charles told them the relevant pieces of Naruto. How they found him. Bits and pieces of the future and what Naruto could do right now.

"The place you live exists in another... dimension. But at the same time it exists in my world as well. Apocalypse watched Naruto for his entire life, watching and waiting for the right time. He watched and learned how to predict your moves and you did exactly as he predicted you would." Erik said with a nod.

"What..." Hiruzen began but he was interrupted.

"What do you gain by telling us all of this? What do you want from us?"

"Do you know how to deal with a teenager with enough power to destroy the world?" Charles asked instead.

"Because that is what your godson is. That is the sort of power he has available to him. I can only thank apocalypse that the man was smart enough so that Naruto could choose to activate another ability of his. That he can master his abilities one by one..." Charles glared at them. "The only way he would activate another before he's ready is if he's made very angry or emotional."

"Do you know that it was Naruto's dream to become Hokage?" Charles asked those present. It only took a moment for them to pick up on the past tense.

"Was?" Hiruzen asked cautiously.

"His dream is to unite all mutants under one banner." Erik said with a smirk. "He wants for them to be a country on its own. To be respected as a country on its own. I wanted to make mutants the ruling race, but if we were to be made a country by ourselves with all rights and advantages that it offers..." Erik allowed himself a very wide smile.

"We would become the most powerful nation by default. Now... Do you want to repair your relation with Naruto... or not?"

"Yes!" Jiraiya, Tsunade and Hiruzen responded immediately.

"Then tell your people the truth. Tell them who Naruto was. What he carried. Tell them that he was taken because of the power he carried so he could be taught how to wield it. Tell them about the threat that apocalypse forms."

"I lack the proof to make any sort of point." Hiruzen pointed out logically. "Look, you made your point and I want to belief you, hell I **do** belief you. But others won't. The other clans won't. And if my own people will doubt my word then the other villages will also doubt my word."

"Then prepare anyway." Erik shrugged. "Prepare for war. We will teach Naruto everything we know and return in four years when he's sixteen."

"I will join you." Jiraiya said immediately. "I abandoned my godson because of duties. I'll be damned if I do so again."

"I agree with the pervert." Tsunade said quietly. "I didn't want to come here but I did so anyway because sensei called in the every favour I owed him." She shrugged. "I'll teach the brat control if nothing else. He's the closest thing I have to family except Shizune, Jiraiya and... sensei." She said after several seconds.

"We know that apocalypse will start a war in the future. We don't know the exact date. We do know that his younger self is active **here**. He's been manipulating things for decades. It's all I can do to disguise my very presence." Charles said slowly. The younger self doesn't know about the lab or Naruto. But that doesn't mean he isn't a very powerful mutant with a God complex. I can guarantee that Naruto will play a role in the war to come."

"What about Kakashi?" Jiraiya said after a moment. "I know that the man is getting into a depression ever since you declared Naruto a criminal. If he knew about this he would want to protect and teach Naruto with everything he knows."

Hiruzen shook his head. His eyes glazing over. "He's supposed to teach Uchiha-sama."

"Did he just..." Jiraiya asked with wide eyes.

Charles unleashed what power he could spare and checked the Hokage's mind for tampering.

"Do you know who Danzo is?" Charles said after a moment. "I suggest you track him down and execute him for treason. He's the one that has managed to control the Hokage to a point. Hiruzen has a very strong mind. Otherwise, Naruto's life would have been even worse.

"Excuse me for a moment." Jiraiya muttered. He walked outside and they heard him tell the secretary council man Danzo's presence was required with great urgency.

"That should take care of that." Jiraiya said with a nod. "Tsunade... Can you use THAT genjutsu on him?"

"But we agreed to..." She protested before she cut herself off. "You're right. He deserves it."

That same night, elder Danzo was rushed to the hospital because of a heart attack. Tsunade managed to keep the man alive but in a coma.

Charles retrieved every bit of useful information he could and 'copied' that knowledge into Jiraiya's, Tsunade's and Hiruzen's minds.

"That... Bastard." Tsunade growled. "Agreed." Jiraiya muttered.

Hiruzen glared at the ground. "Charles, can you... Modify someone's behaviour?"

"Modify... How exactly?" He wanted to know.

"Danzo has done many bad things. But he's also a useful tool we can use from a distance. Change a number of things in his personality... Make his first priority to obey me... Or the next Hokage... The illegal ANBU are already there. They exist. They made the sacrifice as they have. The only thing we can do is not recruit any more but use what we have available."

None of them liked it but they saw the point in it.

"With Jiraiya, Tsunade and Kakashi teaching the boy... He'll grow strong very quickly." Erik spoke up again. "Isn't that too much pressure to put on a boy? How would he even think himself as? A mutant? A ninja?"

"That's his decision to make." Jiraiya spoke up eventually. "I'll let him sign the contract of the Toads."

"And the slugs." Tsunade added.

"And the monkeys." Hiruzen finished. "But only if he's ready. "If I tell them what you told me... I need to get stronger too. I let myself get too weak for my comfort."

"Each of us already has made mutant allies in the outside world." Erik began. "It's going to be difficult for them to want to follow Naruto as a leader.."

"He's not." Charles pointed out. "Not yet at least. Let the boy prove himself. Let him make his own choices."

X

**I'm guessing that the end result is entirely different. Different enough that you can't know where I got it from. A cookie if you tell me the original title...**


	2. Chapter 2

Naruto: evolution

Short summary: Naruto is taken by future Apocalypse to prevent his own defeat. He takes Naruto before he has a chance to mature into the warrior he fears of the future. F-Apocalypse changes Naruto so he would be one of the most powerful warriors of the planet and utterly, completely loyal to him. Fortunately, or unfortunately, Naruto is only found shortly before the brain washing could begin...

Complete summary: Naruto is taken after the forbidden scrolls fiasco by the Apocalypse, who came back in the past after being defeated in the future. Future Apocalypse meant his past self to find Naruto in order to prevent his own defeat. Using all the impressive technologies that future-Apocalypse has at his disposal, he modifies Naruto's genes to have the powers of some of the most powerful mutant of his time. Thankfully his plans are all for naught when Naruto is found just before the brainwashing could begin...

**I feel that the political situation I've described is hard to continue. Naruto is twelve, and right now graduation age is twelve. Even though Hiruzen may as well increase the age of graduation it's entirely possible that the current generation will still graduate at... Twelve. Or maybe not. I already mentioned something of being trained for four years. Jiraiya AND Tsunade are going with Naruto and it takes place during x-men first generation. Specifically during the time the movie is showing. Before Charles and Erik split and before Charles gets stuck in a wheel chair...**

Naruto: evolution

Chapter 02

"So aside from having three of some of the most famous summoning contracts..." Jiraiya began. "Assuming of course our summons agree to share." A pause.

"They will if they are told what we know now." Tsunade pointed out. There is nothing that forbids anyone from having multiple contracts after all." What wasn't said was the fact that having even a single contract gave one a lot of prestige. It had happened before that there were famous shinobi having multiple contracts. But these shinobi were as much respected as they were hated and feared. The amount of fire-power even a single contract offered could do a lot of damage. Let alone three at the same time.

"I have considered your request Hokage-san and I reluctantly agree." Charles said after a moment. Referring to Hiruzen's request that he 'modify' Danzo's behaviour so that he would be completely loyal to Hiruzen first, the village second and anyone else not. If Hiruzen died in the line of duty then that loyalty would be transferred to the whoever would take the place of Hiruzen.

"Consider this a big favour though." Charles warned. "This is pretty much the mental version of rape." Charles glared at the other man. "Just so you'll know what you're asking me to do."

"Thank you Xavier-san." Hiruzen acknowledged. "What about my other old team mates? It... Hurts that Danzo betrayed me like that. I'm not sure what I'll do if my other team mates have betrayed me as well." The additional request was there albeit unvoiced.

Charles closed his eyes and reminded himself that the man he was about to change had done a lot of terrible things. He was about to put on a heavy leash.

Charles closed his eyes and tapped into his power. His senses expanded rapidly, tapping every human present very briefly that gave him a very brief summary of who they were. The summaries in the beginning was nothing more then age, gender and their name. But the more people he touched, the more information he gathered and the more detailed information he could get about people.

Hatake Kakashi. Male. 26 years old.

Sasuke. Male. 12 year old. Nearing breaking point because of pressure of females chasing him. Trauma of event early in life and because of several near rapes with eager females.

No, that wasn't the one who he was looking for. Charles did wonder how the police could let that happen though. No wonder the boy was as closed as he was. The boy was completely paranoid about being forced to marry because of a girl raping him.

Charles sighed and while was at it, he made Sasuke very unattractive to any girl stupid enough to just go after him for his name. Dozens of shinobi all with their own problems, all of them seemingly slipping under the radar. Charles felt like shouting. He kept his focus and searched for his original target. Danzo Shimura. After searching for an additional thirty seconds he finally found the man beneath Konoha.

Charles frowned in surprise when he realized that the man was already under some sort of influence. Something that drove him to make the most extreme decisions out of the options he had. Never compromising and always being completely and utterly ruthless.

Charles squashed that influence with a thought. It honestly scared him to know how easily it was to do something like this. Charles changed the man in ways that would never be discovered until certain questions were asked. Questions they had no reason asking unless they suspected something. Suspecting something wouldn't happen because Danzo would act exactly the way he had.

Charles realized several things though that even if the man would become loyal to Konoha and Hiruzen by extension that his past crimes would see him executed anyway. "How disgusting.." Charles muttered.

Charles realized that whoever or whatever had been the influence earlier had taken advantage of an already ruthless character. Charles showed then and there that he too could do what needed to be done. Danzo would stand trial in a closed session. He would confess his crimes in the next shinobi council session with all clan heads who would then decide his fate. To take advantage of his skills still or to kill him for his actions. His own private army of brainwashed ninja only complicated things further.

Charles double and triple checked what he did. He wanted to make absolutely sure that he made no mistakes. Nodding to himself, Charles knew that things would change greatly in the next few years. Now that Danzo was done, Charles moved onwards to look for the Hokage's old team mates. They too were relatively easy to find. Being two of the more powerful shinobi despite their age they stood out among the younger chakra signatures.

Charles touched their minds very lightly and was very happy to conclude that they hadn't betrayed Hiruzen at all. They were intending to gather evidence to punish Danzo for what he did. Only the man was very good at what he did so they had been forced to distance themselves from Hiruzen in order to get Danzo's trust.

"It is done." Charles announced after a moment. Charles explained what he found to those present. About the compulsions that made him go for the extreme decisions. Once he had explained what he had found within Danzo's mind he touched on the man's crimes.

"Danzo has committed too many crimes to my liking and will confess them in the next private meeting. You can decide then and there if he is useful enough to keep him alive. Your old team mates were trying to gather evidence about them and had to distance themselves from you in order to gain the man's trust."

"What about the compulsions?" Tsunade asked. "Would he have done those things without them?"

"I don't know." Charles admitted. "Certainly there were less extreme options at the time. He most likely would have gone for those. I can't guarantee if he would have taken the eyes of the Uchiha though and I'm certain he wouldn't have demanded all the deaths of your Uchiha clan either."

Hiruzen released a sigh he didn't know he was holding.

"I am very happy to hear that my old friends haven't betrayed me. I don't-... I don't know what I would have done if they had..." Hiruzen paused. "But it doesn't matter because they haven't. That's what is important." He said more to himself then those around him.

"There are a few things I discovered Hokage-san." Charles said calmly. "Many of your shinobi are suffering. Either from trauma of something that happened in their past, peer pressure or they are simply near breaking point of their sanity. Some of your people apply to all of them Hokage-san." Charles said.

"**All** of them." He stressed. "I don't know what you have been doing but snap out of it or a number of your shinobi will snap and the Uchiha massacre is going to seem like a happy day compared to what they might do."

Hiruzen seemed to struggle with something, prompting Charles to take a peek for himself. What he senses was beyond anything he had ever felt before. Dozens of compulsions lay over each other. The man's own natural willpower attempting to overcome them but had been held off ever since they were applied. Charles could sense that the man's willpower had been given a boost but whoever had applied the compulsions had been a genius... And near his own power as well. If not more powerful. With a snarl of contained anger, Charles tore into the compulsions and destroyed them completely. What was left of the man's natural defences attempted to expel his own probe but Charles ignored those attempts and helped them to reinforce their defences instead. Retreating as he was repairing them, Charles let out an exhausted sigh.

Hiruzen's eyes were closed as the man was probably trying to figure out what had just happened. When the man opened his eyes again he was of a whole different character. The man seemed to ooze power though it had suffered because of the compulsions.

"It appears I owe you my thanks. Xavier-san." Hiruzen spoke up for the first time after being freed from the compulsions.

"I will correct those weaknesses you mentioned earlier." The man promised. "I will remind my people why I was chosen to be Hokage at an early age and why I am called the god of shinobi and have a flee on sight order from pretty much every village in the world if they are facing me."

"What are you planning to do with Danzo?" Charles questioned. He felt curious to see what this new version would say.

"What the hell just happened?" Jiraiya demanded. His eyes were wide and surprised. "Someone placed dozens of powerful compulsions on him." Charles explained for the sake of his friend Erik and the two Sannin level shinobi there.

"I removed them." He added though it wasn't necessary any more.

The Hokage's snapped up and focussed on his students. "Jiraiya-kun, Tsunade-chan I'm so sorry for what I did." The man murmured. "I tried to fight them so very hard but I had to save my strength until I could break through them. But the more I stopped fighting... The less power I had to gather. It was an endless spiral downwards..." Hiruzen explained.

"If I had been stronger then maybe I would have been able to stop Orochimaru."

Hiruzen focussed on Charles again. "Something deeper is going on here. Compulsions on me, compulsions on Danzo. Something or someone has been doing everything in their power to destabilize things here. Considering how many enemies Konoha has made in the past wars and decades..."

"Let's move this meeting back to more relevant business shall we?" Erik suggested. "I'm sure that the Hokage is old and wise enough to do what it takes to secure his village then his country followed by securing his allies. But we'll come to that later. There is still much to discuss."

"You have already offered yourselves to teach Naruto. You offered the summon contracts you each have as well as teaching him everything you know. The question is... What is this going to cost me?"

"Nothing." Hiruzen said calmly. "You have gotten rid of those compulsions on me that not even Yamanaka were able to detect. You have disabled one of my biggest political enemies as well have helped the leaf a lot. That's enough payment as far as I'm concerned."

"Actually, you may want to change your mind." Charles told them. "We still haven't touched on a number of important issues."

"Such as?" Jiraiya asked. "Actually, before you answer that, I may not be able to teach Naruto as much as I want. Despite how much I dislike the idea, I spent years building contacts all over the continent. I spent years getting their trust, proving that I can offer shelter for discovered spies should they survive the discovery. If I vanish without as much as an 'by your leave' then all my hard work, twelve years of hard work is going down the drain." Jiraiya told them.

"I already saved dozens of lives thanks to my spies and the information they gave me." Jiraiya said quietly. "It pains me to do this but I don't have much of a choice. I can teach Naruto but I can't stay for four years on end." Jiraiya finished reluctantly.

"I have sufficient resources that you can move back and forward as you wish. Though I would ask not to do it if it isn't required. Should the barrier weaken to the point it breaks... I have no clue what would happen if blood thirsty shinobi will come into contact with a world as modern as our own." Charles told Jiraiya.

"I always have felt that the graduation age of twelve is far too young for peace times." Hiruzen mused. I intend to push them back as much as I can. Possibly to eighteen although that's going to be difficult. Sixteen is a more realistic goal. In any case, I will be pushing for a new minimum age of fourteen at least, fifteen or sixteen if I'm lucky and if I'm really lucky eighteen even. You have two years at minimum to teach Naruto-kun."

"How quickly will we know of the new graduation age?" Erik questioned. A plan was forming itself and it only took a mental nudge for Charles to get a look at it.

"Worst case scenario, Charles and I will teach Naruto for a year. With Jiraiya having the remaining one. Best case scenario will mean we have six years instead should eighteen be the new graduation age of Konoha ninja."

"Exactly." Hiruzen agreed with a nod.

"I say we've made a lot of progress so far except for a number of items still." Charles spoke up again. "We have been deciding this without Naruto's input. He will have to be told about everything we know. Lying to him would be pointless because of the mental powers he inherited from me indirectly."

"What does THAT mean?" Jiraiya demanded. "Minato was in love with Kushina so there is no fucking way that either of them cheated on-"

"Calm down Jiraiya-san." Charles said calmly.

"We'll come to that. Possibly the most important issues of this entire meeting." Erik added.

"Xavier-san is correct though. We have been making decisions for Naruto instead of asking him. I can't imagine him refusing but that was before all of this. He might decide he dislikes Konoha and all of us." Hiruzen finished.

"You've said several times there is something else. Something big. Please get to it so that I can get a good night sleep after getting drunk." Jiraiya requested.

"We already told you that a future version of Apocalypse has come to the past for him and the here and now for us correct?"

"Yes." Hiruzen, Jiraiya and Tsunade agreed.

"That means that he was able to make a stop along the way." Charles continued..

"Which means that Apocalypse was able to visit the continent before it got destroyed..." Erik followed up.

"That means that he could make use of the chaos of the fourth shinobi war to get genetic material." Charles continued from where Erik left off.

"Genetic material that is sufficient for him to make clones with. Enough genetic material that Apocalypse is able to create children of clans of the times and identical copies of the shinobi fighting..." Erik continued.

"The base where we found Naruto is enormous. It has dozens of levels going deeper underground and each level is stretching for miles in every direction. The place is a fortress to get into and the only reason we got to its command centre was because future apocalypse made a mistake. He forgot to protect it from me. I can tell you that thousands of mutant signatures of various levels is something I can't miss. That prompted us to investigate." Charles explained.

"The defences of the base are... Awe-inspiring. Erik told them. I checked the blueprints of the base and it is pretty much impossible to take. It would take weeks of studying its blueprints to find a weak spot. It has entire levels dedicated in growing food and is connected with underground rivers to supply the water. Future Apocalypse did everything in his power to give his younger self every advantage he could." Erik explained.

"Even its defences pale compared to its true treasure." Charles added.

"Clones." Erik said. Upon seeing the confused faces of those present, Erik explained.

"Apocalypse comes from a far off future. Naruto will arrantly live for decades if not centuries to come. Anyway the point is that by that time the technology of cloning has been perfected and apocalypse took full advantage of this. He took genetic samples of every powerful warrior of his time, went back in time and took genetic samples of powerful warriors that were alive then. He continued doing that until he came to the time and place before the continent here was still in one piece. He even went further back in time to get the genetic material of your most powerful warriors..." Erik told them.

"There are two types of genetic material or rather you can do two things with them. You can either use the material to use it to breed. It means that the clone would technically be the son of the genetic material. The other requires a different form of genetic material but it would result in a copy of the person they were before the material was taken. An exact copy except perhaps for the fact that their body would be without scars. Even so, Apocalypse designed a computer system that would already guarantee that the clones would be much faster, much stronger and much smarter then your typical civilian putting them on equal grounds of well trained Genin and that's only when they exit the tube for the first time. Finally they are all taught to obey the orders of the subject of our meeting. Uzumaki Naruto."

"Are you telling me that you have a facility with thousands of shinobi of various clans and origin?" Hiruzen breathed.

"Yes." Charles agreed.

"Of virtually any time and place as well?" Hiruzen insisted.

"Yes." Charles repeated.

"Oh my god." Tsunade breathed.

"Are you telling me that he went back further in time to get the genetic material of famous shinobi of our time?"

"That's what I said." Charles acknowledged.

"This changes everything." Hiruzen spoke up. "You hold into your hands an army of every shinobi that died in the past and future. Exact copies all obeying the orders of Naruto."

"That's right. Now do you see why we came here and why we will visit every village on the continent? They will want a chance for these great shinobi to teach their own. To teach techniques lost through time or through the destruction of clans." Charles told them.

"One thing isn't entirely clear to me." Jiraiya spoke up after Charles. "How are they monitored? What I mean to ask is, how are they grown? How can they be taught if they only exit those... Tubes when they are mature?"

"It's a choice." Charles told them. "Apocalypse didn't have the manpower to teach them. He relied on the fact that his younger self would discover the base, find Naruto, brainwash Naruto and then let all the clones mature until he had an army of mutants at his disposal."

"So essentially we have not only an untold amount of shinobi children but also identical copies of some of our greatest warriors of our history." Tsunade summed up. "Not only that but they are all loyal to Naruto. A boy who might hate Konoha's guts for its actions towards him. To make it even more complicated it's also possible, very likely even that some of the strongest of your own shinobi are maturing there as well."

"Pretty much." Charles agreed.

"What do you want?" Hiruzen asked.

"We need people to defend the base." Charles answered. "Even if its defences are impressive it can still be attacked. No defence is perfect and I'm assuming the same is true for this base."

"I'm willing to send out an entire division of my best ANBU to help secure the base." Hiruzen offered immediately. "They will obey Tsunade's orders as if they were my own. Additionally, you can check their loyalties to stop any traitors from infiltrating the base."

"How many ANBU is a division?"

"Twelve shinobi."

"But to honestly take care of thousands of clones..." Tsunade said quietly. "You would need a hundred times that number to care for even a tiny amount. That's why you will visit other villages." Tsunade realized out loud.

"Twelve shinobi would be like a drop of a bucket when you are trying to fill an ocean." Jiraiya quipped.

Hiruzen shook his head. "I can't miss more then a single division. Even that many will stretch our shinobi thin. We are still recovering from the Kyuubi attack."

"You are planning on recruiting your own people as well aren't you?" Hiruzen spoke up.

"Naturally." Erik agreed.

"This is..." Jiraiya spoke up after a few moments. "I'm sorry but this is too much. We've been here for hours already. I need a break. A drink. Some sleep. Let's continue this conversation tomorrow. Let it all sink in a little." Jiraiya nodded to them and then left in a burst of speed.

"I agree with Jiraiya. Don't tell that pervert I said so though. I'm going to prevent the idiot from drinking himself to death." Tsunade announced. She too left in a sudden burst of speed.

"Can anyone say irony when she says that?" Hiruzen muttered to himself.

"How did you plan to take care of those children anyway?" Hiruzen questioned. He felt tired himself as well but he was too curious not to ask few more questions.

"We were counting on getting as much teachers from the villages as possible. The programming of the clones is very well done. If we change anything to drastic... Neither of us has a single clue what this could do do them. It might make them go nuts when they are mature or it might cause problem in other ways. We don't know and that's the problem. In addition of your people we know a lot of people ourselves. I can check the people we recruit for their loyalty so that wouldn't be a problem." Charles explained.

Charles looked Hiruzen straight in the eye. "Erik and I have spend several hours checking the information held on the computers there. They hold very specific information. Future Apocalypse built that base of his to be his headquarters. It holds anything and everything he could think of to give his younger self any advantage he could think off. Advanced technology. Clones of your shinobi of past and future... Mutants of our own world past and future as well. That base holds an army capable of conquering the world if they are taught and equipped properly. Add to this enough regular soldiers and hardware and victory is nearly guaranteed."

"I see..." Hiruzen murmured. "You are going to train them to protect the world then? Destroy any threat that pops up? Peace under threat?"

"How dare you!" Charles hissed. "It would be no different then knowing there is an army protecting your country. Or police officers keeping the law. They would be neutral and would stop any country that threatens war."

"All loyal to Naruto correct?" Hiruzen asked. "Who would Naruto be loyal to I wonder? In fact, what if Naruto ever goes bad? What if he decides that he is worthy of ruling the world under his rule? That his idea of the future is the proper one? You can't guarantee such a thing now can you?"

"I..." Charles started.

"I can't." He answered after a few moments. "But I sure as hell can try to teach Naruto decent values. Equality between humans and mutants alike, the protection of common civilians so that mutants can live their lives in peace until mutants are just as normal as birds in the sky. Until masked heroes are longer needed. I already am working with my own government to create an organization that would do these things. If these infants grow up and agree to join them and afterwards they can live their own lives in peace..."

"But not if the other villages demand that they join their 'homes' or demand that they produce several natural children to repopulate their clans." Hiruzen argued.

"They can demand all they want Hokage-san, they don't have anything to force my hand." Charles said quietly.

"The only thing they can do is send some of their people to teach their own people past and future and teach them their values. I will personally guarantee that there will be no backstabbing or secretly teaching them to be loyal to any other then Naruto."

"What I'm curious about is why you are so confident in a twelve year old boy." Hiruzen half asked half stated.

"You are doing all of this based on information coming from an enemy. Information you have no way of knowing if it is right or not."

"That's true enough." Erik acknowledged. "But there are many things that support the information there. Weaknesses of Apocalypse himself and how to correct them. Bases he has built and bases he has. Agents he has active. That sort of thing. Charles already checked a number of his agents and they all checked out. They all worked for him."

"I do this because I have seen through the information that Apocalypse recorded the deaths of mutants caused by ignorant humans. Caused by fear and hate. If there is an organization that keeps a world wide law, something that prevents bigotry then many deaths will be prevented."

"But most of all I want them to be prepared for when Apocalypse will be ready. For when he and his allies will make their move."

X

Wow. I had a rough version of four pages and increased that to five and a half pages. Four thousand six hundred words give or take a few dozen. Anyway, I tried to explain a lot issues. I had too because there were a lot of holes previously. The mutants will have a big advantage. They have an enormous base and thousands of soldiers of various ages. Both 'empty' clones and identical copies. These identical copies will be the generals and teaches of the 'empty' clones.

Naruto will be taught and will take the place of Fury as director of S.H.I.E.L.D. He'll have thousands of elite operatives running around the world, all loyal to him. And think about the fact that all of this happens during x-men first generation.

Erik will never go 'Evil' now and he and Charles will remain friends. Everything has changed completely. I must admit that I'm pretty much ignorant of what Apocalypse can do but I'm making him a major villain. He still has a lot of allies, lots of resources and a lot of power to throw around.

This story will probably share the same universe where the avengers film happens as well as the fantastic four and the hulk. I already hinted at other **costumed** heroes and villains alike so they too will exist.

As it is, the good guys have an overwhelming advantage. An advantage I'm unsure will make them too hard to defeat or at least it makes it hard for me to power the villains up as well to make them equal to the good guys. Otherwise it would be boring.


	3. A confrontation

Naruto: evolution

Short summary: Naruto is taken by future Apocalypse to prevent his own defeat. He takes Naruto before he has a chance to mature into the warrior he fears of the future. F-Apocalypse changes Naruto so he would be one of the most powerful warriors of the planet and utterly, completely loyal to him. Fortunately, or unfortunately, Naruto is only found shortly before the brain washing could begin...

Complete summary: Naruto is taken after the forbidden scrolls fiasco by the Apocalypse. Apocalypse, who came back in time after being defeated by Naruto himself. What better irony would there be to take the warrior that would be responsible for your defeat in the future and make said warrior fanatically loyal to you instead? F-Apocalypse prepares a base with all the advanced technologies available to him and places Naruto in the middle of it. Additionally, F-Apocalypse takes genetic material stolen from famous and infamous mutants alike and takes the best of the best and plants it in Naruto's body. Naruto F-Apocalypse knew, was able to adapt to just about anything. Last but not least, F-Apocalypse takes additional genetic material from various people, both warriors and scientists and makes clones loyal to Naruto out of said genetic material. When his past self awakens he would find himself a powerful warrior loyal to him along with an entire army as well.

This story shares with

Spiderman, the Avengers, S.H.I.E.L.D, (movie based) Batman, Superman (partially based on small ville too)

**At this point in time graduation age is twelve. Naruto was taken after he stole the forbidden scroll which means that his generation has already graduated. As shown in the story, Naruto's generation will be considered graduated but will be given extra training after Naruto's sabotage of his academic years is confirmed.**

**Since Hiruzen now has a strong ally in Danzo who was his political enemy before, he can take back his power and show them why he was feared as the god of shinobi. He plans to put the new graduation age on sixteen. This means that Naruto has four years to master some of his power.**

**Naruto has a lot of mutations, but that also means he has to work really hard to get some control over them. Take in the following:**

**Naruto already had large chakra reserves in the manga and anime because of his Uzumaki heritage and because of Kyuubi. Kyuubi was absorbed into the seal and into his chakra reserves completely leaving only a voice in the back of his head. On top of that you have several mutations that he needs to get control over. Mutations that by themselves would already class him as a high A rank warrior. Without control though that high A rank class would be reduced to high c rank if he's lucky. Last but not least, Tsunade is going to stick with Naruto to keep an eye on him. Why would she do that? Naruto is an unique case in the world. Tsunade is the best chakra medic of the elemental countries.**

**That should explain it.**

**At the same time, Tsunade, Jiraiya and Hiruzen are going to step up their training again, study modern medicine (Tsunade) step up his spy network as well as master some of his ninjutsu (Jiraiya) and make himself worthy again of the Kage title. (Hiruzen.)**

Naruto: evolution

Chapter 03

Despite what Charles and Erik thought, F-Apocalypse hadn't bet everything on the base and that which it contained. He had in fact send a timed message to one of his allies from the future. He and mister sinister had fought back to back on occasion so he felt that he owed the man something. Giving him partial information about the future would be the limit of what he felt he owed though.

F-Apocalypse had built another base. One that was even harder to find and was a lot better protected. The location of the base wasn't in any of the computers in his main base except one. Naruto would only be informed of this computer at the end of his training. This guaranteed that Naruto would be loyal to him and that his second base wouldn't be put at risk. If the computer wasn't accessed within forty eight hours after his training would end then it would release a virus that would attack and delete all the information on the network.

This other base contained four of his best warriors. Warriors that would be equal to Naruto by themselves because of their mutation and their skill level. Naruto might outclass them in raw power but his four warriors would be able to defeat him anyway because of their experience and how skilled they were.

His four horse men that represented himself, the end of the world, the Apocalypse would obey him first and Namikaze Naruto second.

F-Apocalypse had done everything in his power to give his past self a decent chance. The base had everything to be self sufficient. It had enough manpower and fire-power to be able to defeat several minor countries, annexing their own power on what he already had. A secure base. An entire army to command. Technologies centuries more advanced then what was available now. When all this was complete, F-Apocalypse died with a smile on his face.

X

Charles and Erik had left after several more meetings. Hiruzen had put the village into lock down and had recalled every shinobi who wasn't on a village critical mission. In a series of bold moves he tracked down every civilian that tricked or took advantage of Naruto in some way. Over pricing, subtle insults. His killing intent washed over the village and reminded them why he was in charge. The civilians that showed regret were given a new chance the ones that didn't vanished and their property was annexed into his private accounts to be given to Naruto later.

Hiruzen had the academy teachers reviewed as well as their lessons. He had the last students grades checked and double checked. If Naruto became so powerful in the future why was it that he was declared a lost case here and now? Once the subtle sabotage was found, he ordered the last generation to be given additional training but they could keep their rank if they passed. If they failed to pass then they would go to the academy until they were sixteen years old.

With his two old team mates at his side, Danzo secretly working with him while still pretending to be his own man, Konoha was a different place in just a few weeks time. This was why he regulated all in village D-rank missions To the last year academy students. All D ranks that were outside the village and low rank C missions were now given to newly graduated Genin teams after the Jounin teacher had taught them enough and they could go through a number of obstacle courses.

X

Erik and Charles returned to the base, accompanied by Jiraiya, Tsunade and a clone of Hiruzen to go to Naruto and explain a few things to him. The boy in question was still floating in the tube completely unaware of the outside world.

"Are you sure it was a wise thing to leave him in that thing?"

"Don't worry about it." Erik said. "We disabled every drug and program that would brainwash him but left useful ones active. Different languages, fighting styles and basic information about the powers he has available to him." Charles added.

"My god.." Tsunade muttered when she noted a wall full with security screens. The security screens showed the clone level. Each tube had clones of various ages and genders.

Tsunade activated the console and after studying it a bit she figured out how to look for something.

"_This base is enormous!" _Tsunade thought to herself. _"It has a separate level for mutant clones, a separate level for your regular guards, then one for soldiers and then one for elite soldiers like our own ANBU."_

After studying it more, Tsunade came to the conclusion that their 'programming' told them to obey Naruto. There was nothing mentioned about Apocalypse. Tsunade remembered that Charles or Erik said that famous shinobi's genetic material was taken as well.

"_I wonder..."_ Tsunade did a search to look for herself, Jiraiya and Orochimaru. She closed her eyes and when she heard the sound that signified that the search was complete she slowly opened them.

She hadn't wanted to believe it but there it was. Three very young children that looked like clones of herself, Jiraiya and Orochimaru.

"Jiraiya!" Tsunade called urgently. Jiraiya looked up from what he was doing. Information that Apocalypse had gathered before their continent was destroyed but was still the future from this point in time. He noticed that Tsunade was staring at a number of screens. The urgency in her voice made him abandon his computer to walk closer.

What he saw on the screens shocked him completely. The security screen showed three different children. All as nude as the day they were born. More importantly he recognized them.

"I didn't want to believe it." Tsunade muttered. "But there you go! Three clones of our selves! Do we... Kill them? We are still alive you know and they might dislike the fact they are clones..."

"Tsunade..." Jiraiya muttered. "Charles told me that the clones are fully aware they are clones. But they aren't US. They aren't us when we were that age. They don't have the personal memories about sensei and the war. More importantly, they don't have our contracts."

"Are..." Tsunade began. She turned and looked at her old team mate. "Are you sure? Are you sure they don't have our memories? They have been cloned out of our genetic material so are you SURE?"

"I..." Jiraiya began. Doubt was beginning to eat at him and he wasn't sure if he could say yes with absolute certainty.

"I can't guarantee it Tsunade-chan." Jiraiya said quietly.

Tsunade looked down at the console again. She searched through it and found a program that would tell her what she wanted to know.

X

Naruto had been moved to the medical level. A number of advanced androids and already completed clones were sleeping there until they were needed. There was enough medical personnel both organic and inorganic to take care of an entire army should they ever be awakened.

Erik and Charles had only just reached this level while Tsunade and Jiraiya were elsewhere.

"The patient is just sleeping sir." One of the cloned doctors declared. "His body is getting rid of the drug that keeps him asleep quickly so I estimate he should wake up within a few hours."

"Very good." Charles acknowledged. "We'll be waiting. Continue to monitor him and if he is waking up I want to be notified immediately."

"Yes sir." The clone acknowledged.

Charles and Erik had downloaded some information on a tablet and a connection to the local network. They had continued to make separate copies of the data-base until they had a complete copy of everything. Charles wanted to examine what he would have done once upon a time if this hadn't happened. What he found discouraged him.

"Erik..." He muttered. Erik who had pretty much done the exact same thing glanced at his friends tablet and realized immediately that they had looked for the same thing.

"I know Charles. But that future will never happen now. I still want to kill Shaw though. But since we know what he intends to do... We can ambush him and kill him before he can kills Darwin. I have an idea though.." Erik looked at Charles and willed him to take a look for himself.

Charles knew his friend well enough to understand what he wanted. He immediately realized that this would be an excellent idea. Pretend to be enemies but really be allies instead. Two groups apart that seemingly dislike each other but at the same time...

"Do what you must Erik." Charles said eventually.

Erik acknowledged it and continued reading.

Neither knew how much time passed when the doctor from earlier cleared his throat to get their attention. "Excuse me, but master Naruto is about to wake."

"_Master Naruto?"_ Both men thought at the same time. The doctor must have seen something in their expressions because he promptly explained.

"All base personnel know exactly who Naruto is. We don't care who he is loyal too because our own loyalty is only to him." The doctor explained with a smile. Then it seemed like the doctor switched from nice to scary. Both men stepped back at the same time because of the sudden change of personality.

"Do keep in mind that even though you stopped Naruto being loyal to lord Apocalypse... You didn't do this for everyone else." The doctor held up his hand to stop them from saying something.

"Lord Apocalypse did miss something though. Perhaps it was because he was injured and couldn't think entirely straight. The fact of the matter is that our first loyalty is to master Naruto. Lord Apocalypse has no authority over any of us. We have been taught through our dreams and through the programming that we have to obey master Naruto and do what it takes to keep him healthy and alive. Don't think because we obeyed your instructions that you can order us around." The doctor paused.

"Don't pity any of us either. Even though Apocalypse was pretty much insane and should be utterly destroyed when you have the chance he made no secret of the fact what we are." The doctor explained.

"We are clones." The doctor declared matter of factly. "It means that any of us is disposable and honestly none of us care about that fact as long as we can take care of our master." The doctor shrugged.

"We are also very aware of the future so we can act as advisor's should master Naruto every seek our advice. The only limitation to us clones is time. Lord Apocalypse wanted his younger self to have an overwhelming amount of man and fire-power. He wanted to clone the same warriors several times but he was too injured to make a good and calm decision about it at the time so he made a snap decision. He ordered us doctors to make the best decision to this. It wasn't much later that he died. Us doctors decided there could be only one of us running around at the same time."

Both men had been listening with utter fascination. "Why didn't you make copies of the same person over and over again?" Erik asked curiously.

"Because that would lead to strive." The doctor shrugged. "Besides, I didn't say there would only be one copy at all right? Let's just say that us clones are connected with each other. If I were to die, then everything I have experienced would be transferred to another me. That new me would probably be slightly different but overall he would be me. It's a form of immortality if you will. As long there is another clone ready we can never die permanently. Now, I think that Naruto is very near the point of consciousness, so if you wanted to be there when he woke up... I already notified Lady Tsunade and master Jiraiya."

Charles and Erik looked at each other before nodding simultaneously. "We will talk about this later doctor." Charles said. "I am very much interested in hearing more from you."

The doctor shrugged. "Just keep in mind what I said master Charles and master Erik." The man said calmly. "Now if you will excuse me, I have work to do." With that statement the man left.

Erik and Charles entered the room where Naruto was sleeping followed by Jiraiya, Tsunade and the clone of Hiruzen who had been meditating to preserve chakra as well as the technique to slowly drain the environment of natural chakra. The latter was a dangerous technique that worked to keep Kage Bunshin working for long periods of times.

"I have recovered to ninety five percent of my chakra." The Hiruzen clone declared. "I should probably make another clone to alert the real me that Naruto is about to wake up. Can I count on you Tsunade-chan to boost the chakra reserves of this clone somewhat? Making a single clone will reduce what I have to nearly forty percent. I'm using chakra faster then I can recover it so without a boost I'll only last for no longer then two hours and that's a really positive guess. An hour would be more likely."

"Sure sensei. Don't worry about it. You are the only one that Naruto knows after all."

Clone Hiruzen nodded and made another version of himself followed by dispelling itself sending what it knew back to its real self in his home.

A few moments later the new clone straightened out. "The real me has received what I learned here perfectly. Please let me handle Naruto if he wakes up. Being surrounded by strangers won't help much. I'm down to thirty eight percent and going down Tsunade-chan. At this rate I won't last another thirty minutes."

Tsunade rolled her eyes but did as he asked. She prepared her chakra and carefully probed the clone knowing that it was very weak and fragile. "Fifty percent." The clone muttered.

Tsunade continued transferring her chakra, making sure to keep the flow steady.

"Seventy five percent." The clone continued.

Tsunade slowed the flow of her chakra and waited for the next report. She sensed that the clone was nearly full.

"Ninety five percent." The cloned reported again. Immediately, Tsunade decreased the chakra flow to an all minimum before cutting it off completely.

"Ninety nine percent." The clone noted. "Was that intentional Tsunade-chan? If so then I find myself truly impressed."

Tsunade snorted in reply. "Are you forgetting that I'm hailed as the best medic currently alive? You did surprise me by reporting ninety percent, I had hoped to hear a lower number but I already calculated how quickly you were filling up by your second report."

The conversation was interrupted when Naruto groaned painfully. Tsunade immediately scanned Naruto and noted that the drug that was keeping him asleep was completely absorbed into his body. It should be only a few minutes maximum for him to wake up fully. She also noted that a great amount of information was being released into his consciousness. It was possible that it could knock him out again.From this point onward it will be entirely from

Naruto's point of view.

Just before groaning painfully.

X

When Naruto found himself waking up he was confused. He knew things he didn't know before and he had already done things on instinct he would never have done before. He had subtly tested his strength in his arms and legs, testing if he was drugged or if he was restrained. He had checked his chakra reserves and while he knew he had lots of the stuff before, now it seemed like an endless ocean compared to before.

Naruto's memories returned of how he had stolen the forbidden scroll and how pathetically easy it has been. _"How I could have fallen for such an obvious plot is something I can't figure out."_ Naruto thought to himself.

Moving on he now knew he wasn't restrained. He wasn't drugged and he felt stronger then ever before. He remembered pretty much everything just until Iruka said something about hating the fox, but after that everything went blank.

Naruto frowned when he could only recall vague images and feelings of terror and fear. Before he realized what he was doing, he instinctively released his chakra as if he were dispelling an illusion and was promptly assaulted by dozens if not hundreds of memories. Naruto found himself being overwhelmed by the sheer amount of information that was assaulting him. It was at this time that one of his mutations activated.

The mutation had always been there and allowed Naruto to adapt to pretty much anything. This mutation helped Naruto to overcome the raw amount of information that was now trying to settle in his subconsciousness and all of this happened in a timespan of minutes.

When the information transfer was about at a third through, Naruto couldn't suppress a groan of pain. The information transferred doubled in its speed and intensity causing his natural mutation to scramble to adapt. By the end of the transfer, Naruto knew he had changed forever.

Seconds ticked passed and Naruto allowed him several moments to let the information settle. He knew that he had many hours of intense meditation before him before he could call on the information he had now available to him.

Naruto's eyes snapped open, the real Naruto charged Jiraiya while clones he had created only a brief moment before charged the others.

Five painful grunts followed each other up rather quickly as each person in the room was slammed into the wall rather painfully. Naruto wasn't too worried though. Each of them was tough enough to handle it. He had carefully adjusted the force he used with each person. Especially Erik, Charles and clone Hiruzen as well.

The real Naruto replaced himself with another clone he had created so that the real he could oversee the others easily.

"Human, Human, clone, mutant and mutant." Naruto summed up. "I do wonder how such people could work together so easily..." He wondered out loud.

"No." Naruto corrected himself as he stared at Jiraiya and Tsunade. "You aren't just human... Both of you have training. Elite training I would say. Probably Jounin level or higher." Naruto reasoned out loud.

"Of course that's what I would say if the information dump of earlier had never happened. I know who you are, Jiraiya of the Sannin. Tsunade of the Sannin. Godfather. Godmother." He summed up.

"I need a name before I kill every single one of you for your treachery against me. Except for the two mutants of course. They get a pass out of my base."

Hiruzen was the first to speak up. Even though he was a clone. He really wished that the real him was here right now. He just knew that the real him could do this a lot better. _"Oh well, at least the real me will get one hell of a headache by the end of this._" Clone Hiruzen reasoned.

"My name is Hiruzen Sarutobi. Third Hokage of Konoha, Naruto-kun. You are Naruto Uzumaki. I don't take threats lightly, I suggest you relax."

Naruto glared at clone Hiruzen. "I didn't ask for YOUR name clone. I was asking for mine. Naruto Uzumaki died when he was betrayed by one of his teachers. I know things now. Many things. Sensitive things. But the tank... Something went wrong. The connection with Apocalypse couldn't implant a connection with him. His words are hollow. Conqueror, killer, murderer... Legacy. It was one of the last things his message said. It'll do fine. From this name forward my name will be Legacy." Naruto declared.

"Now... If you think you are worthy of coming here... Into my base, the legacy of our own people and that of the mutants then prove your strength and try to overcome me." Naruto taunted.

'Clone.' He added with a sneer.

Naruto's clones remained silent but it was obvious they were all battle ready.

"You don't want Apocalypse to command you?" Clone Hiruzen asked curiously. "I do wonder why such a powerful warrior chose you when you can't even pop a clone that doesn't have even ten percent of my true strength.

"Wrong clone." Naruto retorted.

"I adjusted my strength to keep you intact. Or didn't you notice such a trivial thing? I know exactly who you are **traitor**. I feel nothing but contempt for Apocalypse enemies and dislike for you. I will do as I always have done before. My own thing, for my own reasons and just like always I'll do it alone." Naruto said with a hateful sneer.

Then, his personality switched from hostile to barely constrained neutrality.

"Apocalypse imprint failed. Mostly due to the meddling of those two there." Naruto informed them, pointing into the direction of Charles and Erik.

"Without a reason to fight that's truly mine, any fight is as good as any other. So I might as well take yours to begin with. I do wonder now that we are in this situation... Your reason for keep secrets. The identity of my mother. My father. My prisoner before I absorbed him..."

The clone of Hiruzen didn't show any surprise but inwardly he was cringing with each blow. He could only hope that the child before him would see reason. Would be able to see it from a neutral point of view.

"You aren't the child you were before Naruto." Clone Hiruzen observed. "Now, you would be capable of keeping any secret you were told. But before this happened... You would have shouted it for anyone to hear just who your father and mother were before they died. I fully intended to tell you everything after the chuunin exams in a few months time. Regardless if you were even in it or not."

Naruto watched Hiruzen carefully but couldn't see any trace of a lie. "It appears you are telling the truth." The boy observed. "That still doesn't explain why you lied completely. If you had told me you would tell me after the chuunin exams I wouldn't feel as angry as I feel now. You told me you knew nothing of all the questions I asked you. You knew nothing of who my parents were. You denied to have the information as to why I was so disliked bordering on hated in the village. You refused to help me when rumours flew around, about me being a thief or causing untold amount of damage.." Naruto summed up.

"It is true I was a bother. It is true that I annoyed people. All for the sake of attention. Positive or negative I didn't care much as long as I was given SOME attention."

The clone of Hiruzen stared at the ground. "Naruto-kun," The man began quietly. "I know I made mistakes. I am only human. I shouldn't have let it go out of control like that. I should have been firm. I should never have announced your identity as the keeper of the nine-tails in the first place."

Naruto grunted and with a thought all of his cloned popped away. "It will do." Naruto said with a nod. "You are only human just like the rest of us. Just remember that I am only giving you a second chance because even though you lied to me, you also gave me a good time many times. There is only one thing to do before I consider this case closed."

"Oh? What's that?" Clone Hiruzen asked curiously.

"This!" Naruto said. In one smooth motion he smashed his fist into the stomach of the clone, dispelling it instantly.

"Now that feels great!" Naruto exclaimed with a wide grin.

Naruto turned to the rest of those present in the room to find them frozen in place. Naruto blinked several times before he realized what the problem was. With a thought they were released from being paralysed.

Naruto didn't waste time by confronting his so called godparents in the room though.

"Do you have perhaps any good excuse for being absent in my life? After all, you were supposed to take care of me." Naruto asked curiously. All traces of the angry aggressive boy from earlier were completely gone. It was like he had never been that angry to begin with.

"Oh, and call me legacy. Naruto died as far as I am concerned." Naruto, now known as legacy informed them.

Tsunade shrugged. "I was dealing with a lot of things." Tsunade said lightly. "The last people in my life were killed of shortly after each other with similar circumstances. I couldn't handle staying in the village for too long. Still won't as far as I'm concerned. Perhaps in a few years that could change. When I finally snapped out of it, too much time had passed for me to barge into your life. I assumed that Hiruzen-sensei would keep an eye on you." Tsunade shrugged. "That's the sole reason." She added.

Naruto wanted to be angry but he couldn't. It was a valid reason and as much as he wanted to throw a tantrum about it, she was there now.

"What about you?" He asked. Pointing his finger at Jiraiya.

"I was busy." Jiraiya answered. "Konoha was weak. We had lost hundreds of ninja permanently and hundreds more were in the hospital. Our total amount of manpower was cut by a third. That included some of our toughest and strongest people. I was needed to keep up a strong image. I was responsible for wiping up dozens of bandit nests that had cropped up that would have taken a full Jounin squad to destroy otherwise. It was this reason and that reason only that Konoha is still standing. The other villages feared my wrath should they attempt to invade Konoha." Jiraiya shrugged.

"That, and my toad allies would be able to do a LOT of damage should it come down to it. I had been planning to be there when sensei would tell you the truth about things."

"I see..." Naruto murmured. He would give the man a chance. The strategist in him could appreciate the man's sacrifice. Of course the strategist in him also pointed out that he was also grieving. He had lost the man he had trained into the Kage position and since he looked a lot like the man it meant that he couldn't have the time to process it all.

Jiraiya was obviously very aware of these facts and he was aware that Naruto knew that he knew. Still, Naruto nodded and a wordless agreement was made then and there. Don't make a stupid mistake like that again. Not without one hell of a good reason.

Finally, Naruto turned to the last two present. "The both of you I know as well. Charles Xavier. Most powerful mutant in the world with the exception of very few people. Erik Lehnsherr, one of the more powerful mutants in the world. Just what are the two of you doing here? You shouldn't even be aware that this place exists let alone be aware of the hidden elemental continents."

"We found you trhough the amount of mutants hidden here." Charles informed Naruto.

'Oh' Naruto murmured. "That makes a lot of sense indeed."

"Now, I need to rest. I need to meditate. The transfer of raw information has left me exhausted. Count on that the confrontation with..." Here, he paused to consider how to address...

"Right. After the confrontation with gramps and my newly discovered set of godparents." Naruto said eventually."

Tsunade, Jiraiya, Charles and Erik all left the room.

Naruto considered what had just happened. He wasn't tired. Not really. But the events had drained him emotionally. He had acted mostly on instinct. Had let his emotions guide him.

"_That wasn't my best decision."_ Naruto reflected uneasily. _"Even though it felt really good to hit him in the gut, it would have felt even better if I could have gotten hold of the real thing. Of course, if it had been the real thing, I would have gotten my ass kicked all over the place. Mutations notwithstanding."_

Unfortunately for Naruto he was broadcasting his thoughts to just about anyone that was willing to hear it.

"_I could have probably convinced gramps to agree to anything. But no, I just had to hit him in the gut instead. It did feel very nice. He did deserve it to some extent. I wonder if I'll pay for it later?"_ Naruto wondered.

"_Nah!"_ He dismissed the thought. _"If he tries anything he'll risk ruining his new relation with me for petty payback. As long as I don't needle him without need I should be fine."_ Naruto continued his rant.

"_I think that Apocalypse did screw up with me. He tried to make me his best warrior. Even beyond his usual elite four. His four horsemen. Without proper morale support though, even the toughest warrior will crack eventually. I just need to keep up the cool image. Can't let them know there is still something left of the twelve year old in here. I need to remember to answer to legacy only and not to my old name... Not in the beginning at least."_ Naruto reasoned quietly.

"_I wonder if they got any decent ramen here... hmmm Ramen..argh"_ The drool escaped his mouth before he could control himself.

"_I'll visit the kitchen later tonight. Now, let's see if I can practice my telepathy so that I won't start... broadcasting... eventually? Oh fuck."_

It was silent for several long moments before it was broken again.

"_ANYONE THAT REPEATS ANY OF MY PRIVATE THOUGHTS WILL MEET A VERY PAINFUL AND NEVER ENDING END THROUGH CONTINUED CLONING AM I UNDERSTOOD? Never mind, don't bother trying answer verbally or telepathically. Just know that you have been warned._

Charles, Erik, Tsunade and Jiraiya looked at each other and nodded all at the same time. The old Naruto was still in there. Tsunade and Jiraiya didn't know him personally, but at least there was still some of the old, loud and surprising ninja in this one.

X

END

X

There's not a lot of action in this chapter but there is a lot of character development. Naruto is despite everything still only twelve. He isn't his naïve twelve year old self, but his old personality will pop up every now and again.

**Naruto would eventually take over as commander of S.H.I.E.L.D. Not immediately of course**

**Naruto would have lots of agents spread around the world to keep the peace between mutant, normal man and...**


End file.
